LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-665-g17f869bf5e)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
# SRD viscosity demo - rigid star particles

units           lj
atom_style      sphere
atom_modify     map array first big
dimension       2

# read in clusters of rigid bodies

fix             molprop all property/atom mol ghost yes
read_data       data.star fix molprop NULL Molecules
Reading data file ...
  orthogonal box = (-13.293404 -13.293404 -0.5) to (13.293404 13.293404 0.5)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  270 atoms
  read_data CPU = 0.001 seconds

set             type 1 mass 1.0
Setting atom values ...
  270 settings made for mass
group           big type 1
270 atoms in group big
velocity        big create 1.44 87287 loop geom

# equilibrate big particles

pair_style      soft 1.12
pair_coeff      1 1 0.0
pair_coeff      2 2 0.0 0.0
pair_coeff      1 2 0.0 0.0

variable        prefactor equal ramp(0,60)
fix             soft all adapt 1 pair soft a * * v_prefactor

neighbor        0.3 bin
neigh_modify    delay 0 every 1 check yes

fix             1 big rigid molecule
  30 rigid bodies with 270 atoms
fix             2 all enforce2d

#dump           1 all atom 10 dump.star.equil

compute         tbig all temp/sphere
thermo_modify   temp tbig

thermo          100
run             1000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 1.42
  ghost atom cutoff = 1.42
  binsize = 0.71, bins = 38 38 2
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair soft, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/2d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.562 | 5.562 | 5.562 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
         0   1.3101488      0              0              0.21350573     0.32876464   
       100   5.0954142      3.291475       0              4.1218387      1.0087565    
       200   13.041252      4.6176595      0              6.7429006      1.5291618    
       300   11.912727      7.0921814      0              9.0335147      1.9578844    
       400   17.60886       8.3666709      0              11.236263      1.602563     
       500   16.786375      10.630838      0              13.366396      1.7725508    
       600   18.470347      12.42157       0              15.431552      2.1627885    
       700   19.39794       14.349074      0              17.510219      1.9554238    
       800   19.082984      16.464746      0              19.574566      2.2424126    
       900   20.702091      18.253108      0              21.626782      1.8041661    
      1000   18.299191      20.699563      0              23.681654      2.9475408    
Loop time of 0.0474374 on 1 procs for 1000 steps with 270 atoms

Performance: 9106745.092 tau/day, 21080.428 timesteps/s, 5.692 Matom-step/s
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.01287    | 0.01287    | 0.01287    |   0.0 | 27.13
Neigh   | 0.0050573  | 0.0050573  | 0.0050573  |   0.0 | 10.66
Comm    | 0.0024616  | 0.0024616  | 0.0024616  |   0.0 |  5.19
Output  | 0.00025461 | 0.00025461 | 0.00025461 |   0.0 |  0.54
Modify  | 0.024714   | 0.024714   | 0.024714   |   0.0 | 52.10
Other   |            | 0.00208    |            |       |  4.38

Nlocal:            270 ave         270 max         270 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:             73 ave          73 max          73 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:            418 ave         418 max         418 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 418
Ave neighs/atom = 1.5481481
Neighbor list builds = 176
Dangerous builds = 0

#undump         1
unfix           soft
unfix           1
unfix           2

# add small particles as hi density lattice

region          plane block INF INF INF INF -0.001 0.001 units box
lattice         sq 85.0
Lattice spacing in x,y,z = 0.10846523 0.10846523 0.10846523
create_atoms    2 region plane
Created 60025 atoms
  using lattice units in orthogonal box = (-13.293404 -13.293404 -0.5) to (13.293404 13.293404 0.5)
  create_atoms CPU = 0.014 seconds

set             type 2 mass 0.1
Setting atom values ...
  60025 settings made for mass
group           small type 2
60025 atoms in group small
velocity        small create 1.0 593849 loop geom

# delete overlaps
# must set 1-2 cutoff to non-zero value

pair_style      lj/cut 2.5
pair_coeff      1 1 1.0 1.0
pair_coeff      2 2 0.0 1.0 0.0
pair_coeff      1 2 0.0 1.0 0.5

delete_atoms    overlap 0.5 small big
System init for delete_atoms ...
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 2.8
  ghost atom cutoff = 2.8
  binsize = 1.4, bins = 19 19 1
  2 neighbor lists, perpetual/occasional/extra = 1 1 0
  (1) command delete_atoms, occasional
      attributes: full, newton on
      pair build: full/bin/atomonly
      stencil: full/bin/2d
      bin: standard
  (2) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/2d
      bin: standard
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312)
Deleted 16305 atoms, new total = 43990

# SRD run

reset_timestep  0

neighbor        0.3 multi
neigh_modify    delay 0 every 1 check yes

comm_modify     mode multi group big vel yes
neigh_modify    include big

# no pairwise interactions with small particles

pair_style      lj/cut 2.5
pair_coeff      1 1 1.0 1.0
pair_coeff      2 2 0.0 1.0 0.0
pair_coeff      1 2 0.0 1.0 0.0

# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles

timestep        0.001

fix             1 big rigid molecule
  30 rigid bodies with 270 atoms
fix             2 small srd 20 big 1.0 0.25 49894 shift yes 54979                   search 0.2 collision slip inside ignore overlap yes
fix             3 small viscosity 10 x y 50
fix             4 all enforce2d

# diagnostics

uncompute       tbig
compute         tbig big temp/sphere
variable        pebig equal pe*atoms/count(big)
variable        ebig equal etotal*atoms/count(big)
thermo_style    custom step temp f_2[8] etotal v_pebig v_ebig press                 f_2[1] f_2[2] f_2[3] f_2[4] f_2[5]                 f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:904)

thermo_modify   temp tbig
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530)
thermo          1000

#dump           1 all atom 1000 dump.star.mp

#dump           1 all image 1000 image.*.jpg type type zoom 1.6
#dump_modify    1 pad 6 adiam 1 1 adiam 2 0.2

run             10000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2

@Article{Intveld08,
 author =  {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
 title =   {Accurate and Efficient Methods for Modeling Colloidal
            Mixtures in an Explicit Solvent using Molecular Dynamics},
 journal = {Comput.\ Phys.\ Commut.},
 year =    2008,
 volume =  179,
 pages =   {320--329}
}

@article{Shire2020,
 author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
 title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
          Detection Applied to Investigate the Quasi-Static Limit},
 journal = {Computational Particle Mechanics},
 year = {2020}
@article{Monti2022,
 author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava, 
           Ishan and Silbert, Leonardo E. and Grest, Gary S. 
           and Lechman, Jeremy B.},
 title = {Large-scale frictionless jamming with power-law particle 
          size distributions},
 journal = {Phys. Rev. E},
 volume = {106}
 issue = {3}
 year = {2022}
}

- fix srd command: doi:10.1063/1.3419070

@Article{Petersen10,
 author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
 G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
 title =   {Mesoscale Hydrodynamics via Stochastic Rotation
    Dynamics: Comparison with {L}ennard-{J}ones Fluid},
 journal = {J.~Chem.\ Phys.},
 year =    2010,
 volume =  132,
 pages =   174106
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
SRD info:
  SRD/big particles = 43720 270
  big particle diameter max/min = 1 1
  SRD temperature & lamda = 1 0.063245553
  SRD max distance & max velocity = 0.25298221 12.649111
  SRD grid counts: 106 106 1
  SRD grid size: request, actual (xyz) = 0.25, 0.25081894 0.25081894 1
  SRD per actual grid cell = 5.5586635
  SRD viscosity = 0.23558168
  big/SRD mass density ratio = 0.14409881
WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830)
  # of rescaled SRD velocities = 0
  ave/max small velocity = 4.1908497 7.725824
  ave/max big velocity = 2.202625 5.4167964
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 2.8
  ghost atom cutoff = 2.8
  binsize = 26.586808, bins = 1 1 1
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/multi/atomonly/newton
      stencil: half/multi/2d
      bin: multi
Per MPI rank memory allocation (min/avg/max) = 41.29 | 41.29 | 41.29 Mbytes
   Step          Temp          f_2[8]         TotEng        v_pebig         v_ebig         Press          f_2[1]         f_2[2]         f_2[3]         f_2[4]         f_2[5]         f_2[6]         f_2[7]         f_2[8]         f_2[9]        f_2[10]        f_2[11]        f_2[12]    
         0   18.299191      0              0.25067776     37.859815      40.841906      5.7680841      0              0              0              0              0              0              0              0              0              0              0              0            
      1000   0.82328749     8250           0.22908506     37.18973       37.323895      6.0611499      14546          54             54             0              691            28900          11236          8250           1.025654       0              3              0            
      2000   1.314397       8198           0.22953802     37.183497      37.397695      7.6050033      14165          65             65             0              1503           28900          11236          8198           1.0137885      0              3              0            
      3000   1.4327928      8174           0.22973765     37.196727      37.430219      4.8441566      14378          43             43             0              2274           28900          11236          8174           1.0052401      0              5              0            
      4000   1.9637993      8194           0.23036966     37.213164      37.533191      4.9697216      14203          51             51             1              3241           28900          11236          8194           1.0129187      0              245            0            
      5000   1.6886675      8206           0.22987561     37.177507      37.452697      10.972628      14155          56             56             0              4073           28900          11236          8206           1.0024406      0              245            0            
      6000   1.7377657      8197           0.23000322     37.190296      37.473487      6.3971042      14331          57             57             0              4929           28900          11236          8197           1.0094945      0              245            0            
      7000   2.4106224      8199           0.23083719     37.216521      37.609363      5.1070917      14144          49             49             0              5822           28900          11236          8199           1.0074275      0              245            0            
      8000   2.5161884      8202           0.2306663      37.171475      37.581521      12.156127      14263          67             67             0              6667           28900          11236          8202           1.006502       0              245            0            
      9000   2.9100148      8188           0.23124828     37.202115      37.67634       6.1326598      14171          66             67             0              7443           28900          11236          8188           0.99544201     0              245            0            
     10000   3.4714177      8206           0.23192306     37.220567      37.78628       5.1293943      14100          48             49             0              8272           28900          11236          8206           1.0022763      0              245            0            
Loop time of 17.933 on 1 procs for 10000 steps with 43990 atoms

Performance: 48179.444 tau/day, 557.632 timesteps/s, 24.530 Matom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.22008    | 0.22008    | 0.22008    |   0.0 |  1.23
Neigh   | 0.054046   | 0.054046   | 0.054046   |   0.0 |  0.30
Comm    | 0.20917    | 0.20917    | 0.20917    |   0.0 |  1.17
Output  | 0.001317   | 0.001317   | 0.001317   |   0.0 |  0.01
Modify  | 17.275     | 17.275     | 17.275     |   0.0 | 96.33
Other   |            | 0.1731     |            |       |  0.97

Nlocal:          43990 ave       43990 max       43990 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:            122 ave         122 max         122 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:           1569 ave        1569 max        1569 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 1569
Ave neighs/atom = 0.035667197
Neighbor list builds = 500
Dangerous builds = 0
Total wall time: 0:00:19
